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We report the preparation of native polythiophene (n-PT)/[6, 6]-phenyl-C61-butyric acid methyl ester (PCBM) composite nanoparticles from a poly[3-(2-methylhex-2-yl)oxy-carbonyldithiophene] (P3MHOCT)/PCBM aqueous dispersion prepared from an ultrasonically generated emulsion. The subsequent steps involve both ultrasonic generation of microdroplets in argon as a carrier gas and drying followed by thermocleaving of the P3MHOCT component in the gas phase. The chemical transition from P3MHOCT to n-PT was confirmed by Fourier transform infrared (FTIR) spectroscopy. The morphology and size of n-PT/PCBM nanoparticles were determined by atomic force microscopy (AFM), small-angle x-ray scattering (SAXS) and grazing incidence SAXS (GISAXS), giving an average size of ~ 140 nm. The GISAXS results reveal that n-PT/PCBM nanoparticles pack in an ordered structure as opposed to the P3MHOCT/PCBM nanoparticles. The successful vapour-phase preparation of phase-separated n-PT/PCBM nanoparticles provides a new route to all-aqueous processing of conjugated materials relevant to efficient polymer solar cells with long operational stability. The use of ultrasound was involved in both liquid and gas phases demonstrating it as a low-cost processing method.